YF <- readRDS("../data_clean/YFcases/YFlong.rds")
brazil <- readOGR("../data_processingScripts/municipios_2010", "municipios_2010")
## OGR data source with driver: ESRI Shapefile
## Source: "../data_processingScripts/municipios_2010", layer: "municipios_2010"
## with 5564 features
## It has 7 fields
## Integer64 fields read as strings: id
### correct ibg codes (like FIPS)
# the ibg codes in the shapefile have an extra digit at the end, so we just subset the first six digits from the shapefile
brazil@data$muni.no <- as.numeric(as.character(substr(brazil@data$codigo_ibg,1,6)))
Map of Number of Cases per Muni from 2001-2014
# calculate total cases per muni
totCase <- YF %>%
filter(cal.month<13) %>%
group_by(muni.no) %>%
summarise(totalCases=sum(case, na.rm=T))
# add to shapefile
brazilYF <- merge(brazil, totCase, by="muni.no")
#create color palette
colpal <- colorNumeric("Set1", domain = c(1,44))
#create popups
casePop <- paste0(brazilYF@data$nome,
"<br><strong>", brazilYF@data$totalCases,
"</strong> Cases from 2001-2014.")
leaflet(data=brazilYF) %>%
addPolygons(color = "#444444", weight = 1, smoothFactor = 0.5,
opacity = 1.0, fillOpacity = 0.75,
fillColor = ~colpal(totalCases),
highlightOptions = highlightOptions(color = "white", weight = 2,
bringToFront = TRUE),
popup=casePop) %>%
addProviderTiles(providers$CartoDB.Positron)
## Warning in colpal(totalCases): Some values were outside the color scale and
## will be treated as NA